Starting phenix.real_space_refine on Thu Aug 6 20:12:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbl_16544/08_2026/8cbl_16544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbl_16544/08_2026/8cbl_16544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cbl_16544/08_2026/8cbl_16544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbl_16544/08_2026/8cbl_16544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbl_16544/08_2026/8cbl_16544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbl_16544/08_2026/8cbl_16544.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 1.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 94 5.49 5 S 86 5.16 5 C 10566 2.51 5 N 3025 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17260 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5400 Classifications: {'peptide': 692} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 648} Chain breaks: 1 Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2442 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 8, 'TRANS': 285} Chain: "T" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1823 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 21, 'rna3p': 64} Chain breaks: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.18 Number of scatterers: 17260 At special positions: 0 Unit cell: (102.364, 121.272, 165.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 86 16.00 P 94 15.00 O 3488 8.00 N 3025 7.00 C 10566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 712.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 900 " pdb="ZN ZN E 900 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 900 " - pdb=" ND1 HIS E 724 " 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3658 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 14 sheets defined 49.9% alpha, 13.0% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.698A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.406A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.874A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.601A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.634A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.809A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.861A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.439A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.709A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.639A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.591A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.766A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 137 removed outlier: 3.648A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.406A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.838A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.575A pdb=" N GLY D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.481A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.645A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 90 through 98 removed outlier: 3.513A pdb=" N LEU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.708A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.979A pdb=" N ILE E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.674A pdb=" N LEU E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 322 Proline residue: E 319 - end of helix removed outlier: 4.101A pdb=" N GLU E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 330 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 362 removed outlier: 4.111A pdb=" N PHE E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY E 362 " --> pdb=" O MET E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 3.720A pdb=" N LEU E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE E 392 " --> pdb=" O GLN E 388 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 455 through 470 Processing helix chain 'E' and resid 473 through 477 removed outlier: 3.706A pdb=" N LYS E 476 " --> pdb=" O PRO E 473 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 473 through 477' Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 554 through 570 removed outlier: 3.547A pdb=" N ILE E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.714A pdb=" N LYS E 585 " --> pdb=" O PRO E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'E' and resid 607 through 611 Processing helix chain 'E' and resid 618 through 632 removed outlier: 3.622A pdb=" N CYS E 632 " --> pdb=" O LEU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 677 Processing helix chain 'E' and resid 693 through 701 Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 760 through 762 No H-bonds generated for 'chain 'E' and resid 760 through 762' Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 794 Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 126 through 168 removed outlier: 3.815A pdb=" N GLU F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 182 through 202 Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.706A pdb=" N MET F 215 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 237 removed outlier: 3.587A pdb=" N ASN F 237 " --> pdb=" O TRP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 Processing helix chain 'F' and resid 277 through 282 removed outlier: 3.609A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 330 removed outlier: 3.663A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.390A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.337A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 12 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL B 89 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 14 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.423A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 148 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET C 194 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE C 150 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C 196 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN C 152 " --> pdb=" O ILE C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.395A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 167 removed outlier: 6.580A pdb=" N CYS E 136 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ARG E 166 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 138 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL E 58 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 178 through 185 removed outlier: 6.205A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA E 305 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL E 341 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL E 307 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET E 343 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 309 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AB3, first strand: chain 'E' and resid 602 through 605 removed outlier: 6.161A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU E 577 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER E 511 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE E 543 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 513 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU E 512 " --> pdb=" O ASN E 505 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN E 505 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU E 514 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU E 503 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 634 through 641 removed outlier: 6.465A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.603A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3780 1.33 - 1.45: 3938 1.45 - 1.57: 9724 1.57 - 1.69: 183 1.69 - 1.81: 136 Bond restraints: 17761 Sorted by residual: bond pdb=" CA SER E 507 " pdb=" CB SER E 507 " ideal model delta sigma weight residual 1.535 1.463 0.071 1.36e-02 5.41e+03 2.75e+01 bond pdb=" CE1 HIS E 724 " pdb=" NE2 HIS E 724 " ideal model delta sigma weight residual 1.321 1.280 0.041 1.00e-02 1.00e+04 1.67e+01 bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.579 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O3 NAD C 301 " pdb=" PA NAD C 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 17756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 23610 1.41 - 2.82: 687 2.82 - 4.22: 158 4.22 - 5.63: 26 5.63 - 7.04: 8 Bond angle restraints: 24489 Sorted by residual: angle pdb=" C1' U T 52 " pdb=" N1 U T 52 " pdb=" C2 U T 52 " ideal model delta sigma weight residual 117.70 123.42 -5.72 1.20e+00 6.94e-01 2.27e+01 angle pdb=" CA HIS E 724 " pdb=" CB HIS E 724 " pdb=" CG HIS E 724 " ideal model delta sigma weight residual 113.80 109.19 4.61 1.00e+00 1.00e+00 2.13e+01 angle pdb=" C ASN E 723 " pdb=" N HIS E 724 " pdb=" CA HIS E 724 " ideal model delta sigma weight residual 122.93 115.97 6.96 1.51e+00 4.39e-01 2.13e+01 angle pdb=" N1 C T 68 " pdb=" C2 C T 68 " pdb=" O2 C T 68 " ideal model delta sigma weight residual 118.90 121.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O5' C T 50 " pdb=" C5' C T 50 " pdb=" C4' C T 50 " ideal model delta sigma weight residual 109.40 112.67 -3.27 8.00e-01 1.56e+00 1.68e+01 ... (remaining 24484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.76: 10364 30.76 - 61.52: 466 61.52 - 92.28: 84 92.28 - 123.04: 5 123.04 - 153.80: 1 Dihedral angle restraints: 10920 sinusoidal: 5226 harmonic: 5694 Sorted by residual: dihedral pdb=" O4' C T 50 " pdb=" C1' C T 50 " pdb=" N1 C T 50 " pdb=" C2 C T 50 " ideal model delta sinusoidal sigma weight residual -128.00 -59.52 -68.48 1 1.70e+01 3.46e-03 2.10e+01 dihedral pdb=" CA VAL F 206 " pdb=" C VAL F 206 " pdb=" N PHE F 207 " pdb=" CA PHE F 207 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLN F 343 " pdb=" C GLN F 343 " pdb=" N TRP F 344 " pdb=" CA TRP F 344 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2208 0.042 - 0.084: 384 0.084 - 0.126: 275 0.126 - 0.169: 11 0.169 - 0.211: 4 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA TYR F 135 " pdb=" N TYR F 135 " pdb=" C TYR F 135 " pdb=" CB TYR F 135 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C2' SAH F 501 " pdb=" C1' SAH F 501 " pdb=" C3' SAH F 501 " pdb=" O2' SAH F 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" C3' G T 49 " pdb=" C4' G T 49 " pdb=" O3' G T 49 " pdb=" C2' G T 49 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 2879 not shown) Planarity restraints: 2847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.045 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.010 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.023 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 724 " 0.005 2.00e-02 2.50e+03 2.70e-02 1.10e+01 pdb=" CG HIS E 724 " -0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS E 724 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS E 724 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS E 724 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS E 724 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.027 2.00e-02 2.50e+03 1.55e-02 4.79e+00 pdb=" C2N NAD B 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " -0.012 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " -0.011 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.024 2.00e-02 2.50e+03 ... (remaining 2844 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 111 2.49 - 3.09: 12999 3.09 - 3.70: 28376 3.70 - 4.30: 41708 4.30 - 4.90: 65728 Nonbonded interactions: 148922 Sorted by model distance: nonbonded pdb=" O2' G T 49 " pdb=" O5' C T 50 " model vdw 1.890 3.040 nonbonded pdb=" O2' U T 51 " pdb=" O5' U T 52 " model vdw 1.945 3.040 nonbonded pdb=" O2' A T 3 " pdb=" OP1 A T 4 " model vdw 2.056 3.040 nonbonded pdb=" O2' C T 69 " pdb=" OP2 G T 70 " model vdw 2.088 3.040 nonbonded pdb=" O2' U T 51 " pdb=" O3' U T 52 " model vdw 2.132 3.040 ... (remaining 148917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.562 17763 Z= 0.244 Angle : 0.588 7.041 24489 Z= 0.372 Chirality : 0.043 0.211 2882 Planarity : 0.004 0.038 2847 Dihedral : 17.015 153.803 7262 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1992 helix: 1.80 (0.18), residues: 846 sheet: -0.42 (0.29), residues: 308 loop : -0.38 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.020 0.001 TYR F 135 PHE 0.014 0.001 PHE E 77 TRP 0.010 0.001 TRP E 587 HIS 0.042 0.001 HIS E 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (17761) covalent geometry : angle 0.58846 / 0.37 (24489) hydrogen bonds : bond 0.15383 / 10.91 ( 823) hydrogen bonds : angle 6.66433 / 4.78 ( 2290) metal coordination : bond 0.39713 / 18.91 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7985 (mtpp) REVERT: E 57 THR cc_start: 0.7803 (t) cc_final: 0.7442 (t) REVERT: E 69 ASP cc_start: 0.7392 (p0) cc_final: 0.6669 (p0) REVERT: E 83 TYR cc_start: 0.6638 (m-80) cc_final: 0.5521 (m-80) REVERT: E 370 LEU cc_start: 0.7764 (tp) cc_final: 0.7152 (tp) outliers start: 0 outliers final: 1 residues processed: 479 average time/residue: 0.5241 time to fit residues: 281.5928 Evaluate side-chains 317 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 633 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN C 260 GLN D 152 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 461 GLN E 589 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN F 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072477 restraints weight = 45509.332| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.32 r_work: 0.2818 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17763 Z= 0.188 Angle : 0.751 12.600 24489 Z= 0.376 Chirality : 0.047 0.520 2882 Planarity : 0.005 0.054 2847 Dihedral : 15.931 147.242 3631 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.85 % Allowed : 14.58 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1992 helix: 1.80 (0.18), residues: 851 sheet: -0.47 (0.28), residues: 301 loop : -0.49 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 781 TYR 0.028 0.002 TYR E 83 PHE 0.032 0.002 PHE F 97 TRP 0.022 0.002 TRP E 587 HIS 0.016 0.002 HIS E 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (17761) covalent geometry : angle 0.75125 / 0.38 (24489) hydrogen bonds : bond 0.05805 / 4.02 ( 823) hydrogen bonds : angle 5.54967 / 3.96 ( 2290) metal coordination : bond 0.02173 / 1.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 360 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8852 (m-30) cc_final: 0.8611 (m-30) REVERT: A 143 GLN cc_start: 0.9064 (mp10) cc_final: 0.8761 (mp10) REVERT: B 41 ASP cc_start: 0.8673 (t0) cc_final: 0.8172 (t0) REVERT: C 160 GLU cc_start: 0.8922 (pm20) cc_final: 0.8458 (pm20) REVERT: C 194 MET cc_start: 0.9001 (mmm) cc_final: 0.8646 (mmp) REVERT: E 77 PHE cc_start: 0.9164 (p90) cc_final: 0.8857 (p90) REVERT: E 98 HIS cc_start: 0.8870 (m90) cc_final: 0.8598 (m90) REVERT: E 130 GLU cc_start: 0.9012 (tp30) cc_final: 0.8807 (tp30) REVERT: E 239 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7524 (tp) REVERT: E 316 PHE cc_start: 0.9031 (m-80) cc_final: 0.8439 (m-80) REVERT: E 326 PHE cc_start: 0.9080 (m-10) cc_final: 0.8797 (m-10) REVERT: E 384 LYS cc_start: 0.9436 (ttpp) cc_final: 0.9227 (ttpp) REVERT: E 385 ILE cc_start: 0.9732 (pp) cc_final: 0.9512 (pp) REVERT: E 449 GLU cc_start: 0.9021 (pt0) cc_final: 0.8732 (pt0) REVERT: E 547 LEU cc_start: 0.8734 (tp) cc_final: 0.8469 (tp) REVERT: E 667 THR cc_start: 0.7730 (t) cc_final: 0.7429 (m) REVERT: F 114 GLU cc_start: 0.9277 (pm20) cc_final: 0.8611 (pm20) outliers start: 30 outliers final: 12 residues processed: 375 average time/residue: 0.5438 time to fit residues: 229.2186 Evaluate side-chains 307 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 294 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 20 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 chunk 139 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 ASN B 215 ASN C 260 GLN E 117 ASN E 366 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 527 HIS E 589 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072960 restraints weight = 46454.323| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.37 r_work: 0.2841 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17763 Z= 0.153 Angle : 0.700 11.685 24489 Z= 0.357 Chirality : 0.045 0.476 2882 Planarity : 0.005 0.077 2847 Dihedral : 15.853 151.373 3629 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.20 % Allowed : 16.42 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1992 helix: 1.68 (0.18), residues: 852 sheet: -0.48 (0.27), residues: 301 loop : -0.60 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 226 TYR 0.025 0.002 TYR E 59 PHE 0.027 0.002 PHE E 521 TRP 0.023 0.002 TRP E 587 HIS 0.009 0.001 HIS E 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (17761) covalent geometry : angle 0.70002 / 0.36 (24489) hydrogen bonds : bond 0.04926 / 3.36 ( 823) hydrogen bonds : angle 5.37441 / 3.82 ( 2290) metal coordination : bond 0.00445 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8858 (m-30) cc_final: 0.8607 (m-30) REVERT: A 143 GLN cc_start: 0.9096 (mp10) cc_final: 0.8748 (mp10) REVERT: B 41 ASP cc_start: 0.8657 (t0) cc_final: 0.8405 (t0) REVERT: B 70 ASP cc_start: 0.9247 (m-30) cc_final: 0.9035 (m-30) REVERT: C 104 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9000 (pttm) REVERT: C 194 MET cc_start: 0.8971 (mmm) cc_final: 0.8688 (mmp) REVERT: C 232 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8745 (mt-10) REVERT: D 28 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8869 (mt-10) REVERT: D 68 GLU cc_start: 0.8611 (pm20) cc_final: 0.8322 (tt0) REVERT: E 77 PHE cc_start: 0.9185 (p90) cc_final: 0.8894 (p90) REVERT: E 98 HIS cc_start: 0.8830 (m90) cc_final: 0.8579 (m90) REVERT: E 109 PHE cc_start: 0.9009 (m-80) cc_final: 0.8540 (m-80) REVERT: E 124 MET cc_start: 0.9333 (mmm) cc_final: 0.9108 (mmm) REVERT: E 239 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7492 (tp) REVERT: E 250 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7790 (mttt) REVERT: E 264 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9111 (mp) REVERT: E 316 PHE cc_start: 0.8985 (m-80) cc_final: 0.8431 (m-80) REVERT: E 326 PHE cc_start: 0.9071 (m-10) cc_final: 0.8771 (m-80) REVERT: E 442 ASN cc_start: 0.9368 (t0) cc_final: 0.9066 (t0) REVERT: E 445 GLU cc_start: 0.9276 (tp30) cc_final: 0.9053 (tp30) REVERT: E 449 GLU cc_start: 0.8971 (pt0) cc_final: 0.8683 (pt0) REVERT: E 667 THR cc_start: 0.7641 (t) cc_final: 0.7365 (m) REVERT: E 700 LYS cc_start: 0.9486 (mmtt) cc_final: 0.9231 (pptt) REVERT: E 750 MET cc_start: 0.8426 (mtp) cc_final: 0.8209 (mtp) REVERT: E 763 LEU cc_start: 0.9630 (mt) cc_final: 0.9315 (pp) REVERT: E 781 ARG cc_start: 0.8928 (ptp-170) cc_final: 0.8277 (ptp-170) outliers start: 52 outliers final: 21 residues processed: 365 average time/residue: 0.4679 time to fit residues: 194.3193 Evaluate side-chains 316 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 779 GLU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 205 optimal weight: 30.0000 chunk 165 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 147 optimal weight: 0.0370 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.071839 restraints weight = 46160.693| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.35 r_work: 0.2824 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17763 Z= 0.164 Angle : 0.689 11.980 24489 Z= 0.350 Chirality : 0.045 0.500 2882 Planarity : 0.005 0.056 2847 Dihedral : 15.762 154.218 3629 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.01 % Allowed : 18.02 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1992 helix: 1.66 (0.18), residues: 852 sheet: -0.51 (0.28), residues: 297 loop : -0.55 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 782 TYR 0.018 0.002 TYR E 354 PHE 0.028 0.002 PHE E 77 TRP 0.021 0.002 TRP E 587 HIS 0.008 0.001 HIS E 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (17761) covalent geometry : angle 0.68928 / 0.35 (24489) hydrogen bonds : bond 0.04699 / 3.19 ( 823) hydrogen bonds : angle 5.31869 / 3.78 ( 2290) metal coordination : bond 0.00316 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8479 (tp30) REVERT: A 143 GLN cc_start: 0.9118 (mp10) cc_final: 0.8777 (mp10) REVERT: B 28 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8734 (mt-10) REVERT: B 41 ASP cc_start: 0.8699 (t0) cc_final: 0.8420 (t0) REVERT: C 104 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9063 (pttt) REVERT: C 160 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: C 194 MET cc_start: 0.8983 (mmm) cc_final: 0.8725 (mmp) REVERT: D 28 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8861 (mt-10) REVERT: D 113 ASP cc_start: 0.9212 (m-30) cc_final: 0.8866 (m-30) REVERT: E 75 TYR cc_start: 0.8422 (t80) cc_final: 0.8221 (t80) REVERT: E 77 PHE cc_start: 0.9273 (p90) cc_final: 0.8877 (p90) REVERT: E 104 ARG cc_start: 0.9288 (pmm-80) cc_final: 0.8949 (pmm-80) REVERT: E 109 PHE cc_start: 0.9055 (m-80) cc_final: 0.8548 (m-80) REVERT: E 115 TRP cc_start: 0.9367 (t-100) cc_final: 0.9074 (t-100) REVERT: E 239 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7875 (mt) REVERT: E 250 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7899 (mttt) REVERT: E 280 ASP cc_start: 0.8630 (m-30) cc_final: 0.8066 (p0) REVERT: E 316 PHE cc_start: 0.8991 (m-80) cc_final: 0.8425 (m-80) REVERT: E 326 PHE cc_start: 0.9114 (m-10) cc_final: 0.8791 (m-80) REVERT: E 358 MET cc_start: 0.9218 (tpp) cc_final: 0.8990 (mmm) REVERT: E 412 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.6499 (mp) REVERT: E 442 ASN cc_start: 0.9387 (t0) cc_final: 0.9096 (t0) REVERT: E 445 GLU cc_start: 0.9283 (tp30) cc_final: 0.9001 (tp30) REVERT: E 449 GLU cc_start: 0.8999 (pt0) cc_final: 0.8635 (pt0) REVERT: E 483 ILE cc_start: 0.9109 (mp) cc_final: 0.8716 (mm) REVERT: E 547 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8381 (tt) REVERT: E 750 MET cc_start: 0.8441 (mtp) cc_final: 0.8237 (mtp) REVERT: E 778 MET cc_start: 0.9367 (mmm) cc_final: 0.8965 (mmm) REVERT: F 146 ARG cc_start: 0.9403 (tpp-160) cc_final: 0.8969 (mmp80) REVERT: F 314 ASP cc_start: 0.9110 (p0) cc_final: 0.8483 (p0) outliers start: 49 outliers final: 23 residues processed: 344 average time/residue: 0.4183 time to fit residues: 164.7331 Evaluate side-chains 311 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 GLN C 260 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072497 restraints weight = 45902.537| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.33 r_work: 0.2843 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17763 Z= 0.144 Angle : 0.694 14.205 24489 Z= 0.352 Chirality : 0.045 0.486 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.714 157.385 3629 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.83 % Allowed : 19.74 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1992 helix: 1.71 (0.18), residues: 852 sheet: -0.54 (0.28), residues: 306 loop : -0.54 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 782 TYR 0.021 0.002 TYR E 354 PHE 0.043 0.002 PHE E 361 TRP 0.019 0.002 TRP E 587 HIS 0.007 0.001 HIS E 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17761) covalent geometry : angle 0.69430 / 0.35 (24489) hydrogen bonds : bond 0.04489 / 3.04 ( 823) hydrogen bonds : angle 5.20282 / 3.70 ( 2290) metal coordination : bond 0.00365 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 316 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8490 (tp30) REVERT: A 143 GLN cc_start: 0.9112 (mp10) cc_final: 0.8777 (mp10) REVERT: A 160 GLU cc_start: 0.9012 (pm20) cc_final: 0.8502 (pm20) REVERT: A 211 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7572 (tp30) REVERT: B 70 ASP cc_start: 0.9275 (m-30) cc_final: 0.9041 (m-30) REVERT: C 104 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9054 (pttm) REVERT: C 194 MET cc_start: 0.8978 (mmm) cc_final: 0.8760 (mmp) REVERT: D 113 ASP cc_start: 0.9190 (m-30) cc_final: 0.8848 (m-30) REVERT: E 97 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8993 (tm-30) REVERT: E 104 ARG cc_start: 0.9288 (pmm-80) cc_final: 0.8970 (pmm-80) REVERT: E 109 PHE cc_start: 0.9027 (m-80) cc_final: 0.8716 (m-80) REVERT: E 115 TRP cc_start: 0.9397 (t-100) cc_final: 0.9170 (t-100) REVERT: E 239 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7477 (tt) REVERT: E 250 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (mttt) REVERT: E 316 PHE cc_start: 0.8965 (m-80) cc_final: 0.8396 (m-80) REVERT: E 326 PHE cc_start: 0.9111 (m-10) cc_final: 0.8769 (m-80) REVERT: E 361 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7451 (t80) REVERT: E 412 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.6583 (mp) REVERT: E 442 ASN cc_start: 0.9385 (t0) cc_final: 0.9090 (t0) REVERT: E 445 GLU cc_start: 0.9290 (tp30) cc_final: 0.8989 (tp30) REVERT: E 449 GLU cc_start: 0.8994 (pt0) cc_final: 0.8624 (pt0) REVERT: E 483 ILE cc_start: 0.9163 (mp) cc_final: 0.8758 (mm) REVERT: E 649 PHE cc_start: 0.8787 (m-80) cc_final: 0.8459 (m-80) REVERT: E 651 CYS cc_start: 0.8360 (t) cc_final: 0.7751 (p) REVERT: E 771 PHE cc_start: 0.8821 (m-10) cc_final: 0.8549 (m-10) REVERT: F 146 ARG cc_start: 0.9408 (tpp-160) cc_final: 0.8963 (mmp80) outliers start: 46 outliers final: 17 residues processed: 340 average time/residue: 0.4405 time to fit residues: 171.3048 Evaluate side-chains 318 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 361 PHE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 156 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 189 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.072210 restraints weight = 45913.373| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.32 r_work: 0.2839 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17763 Z= 0.151 Angle : 0.686 12.383 24489 Z= 0.350 Chirality : 0.045 0.486 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.678 161.670 3629 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.58 % Allowed : 21.40 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1992 helix: 1.76 (0.18), residues: 849 sheet: -0.50 (0.28), residues: 303 loop : -0.47 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 781 TYR 0.019 0.001 TYR E 354 PHE 0.043 0.002 PHE E 77 TRP 0.027 0.002 TRP E 433 HIS 0.008 0.001 HIS E 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (17761) covalent geometry : angle 0.68606 / 0.35 (24489) hydrogen bonds : bond 0.04356 / 2.96 ( 823) hydrogen bonds : angle 5.12165 / 3.64 ( 2290) metal coordination : bond 0.00428 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8535 (tp30) REVERT: A 142 ASP cc_start: 0.8800 (t0) cc_final: 0.8599 (t0) REVERT: A 143 GLN cc_start: 0.9135 (mp10) cc_final: 0.8788 (mp10) REVERT: A 211 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7597 (tp30) REVERT: B 70 ASP cc_start: 0.9273 (m-30) cc_final: 0.9024 (m-30) REVERT: E 92 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8884 (tm-30) REVERT: E 97 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9013 (tm-30) REVERT: E 104 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8937 (pmm-80) REVERT: E 239 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7567 (pp) REVERT: E 243 PHE cc_start: 0.8376 (m-10) cc_final: 0.8109 (m-10) REVERT: E 250 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (mttt) REVERT: E 280 ASP cc_start: 0.8684 (m-30) cc_final: 0.8098 (p0) REVERT: E 326 PHE cc_start: 0.9088 (m-10) cc_final: 0.8823 (m-80) REVERT: E 361 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7302 (t80) REVERT: E 412 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.6907 (mp) REVERT: E 442 ASN cc_start: 0.9391 (t0) cc_final: 0.9092 (t0) REVERT: E 445 GLU cc_start: 0.9303 (tp30) cc_final: 0.8913 (OUTLIER) REVERT: E 449 GLU cc_start: 0.8994 (pt0) cc_final: 0.8493 (pt0) REVERT: E 483 ILE cc_start: 0.9140 (mp) cc_final: 0.8725 (mm) REVERT: E 561 GLN cc_start: 0.9617 (mm-40) cc_final: 0.9251 (tp-100) REVERT: E 649 PHE cc_start: 0.8781 (m-80) cc_final: 0.8163 (m-80) REVERT: E 771 PHE cc_start: 0.8820 (m-10) cc_final: 0.8480 (m-10) REVERT: E 778 MET cc_start: 0.9330 (mmm) cc_final: 0.8968 (mmm) REVERT: E 782 ARG cc_start: 0.9203 (ptp-170) cc_final: 0.8919 (ptp-170) REVERT: E 784 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8820 (tppt) REVERT: F 146 ARG cc_start: 0.9402 (tpp-160) cc_final: 0.8950 (mmp80) outliers start: 42 outliers final: 21 residues processed: 326 average time/residue: 0.4194 time to fit residues: 155.4170 Evaluate side-chains 316 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 361 PHE Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 46 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 175 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071982 restraints weight = 45701.880| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.33 r_work: 0.2834 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17763 Z= 0.154 Angle : 0.694 13.800 24489 Z= 0.352 Chirality : 0.045 0.486 2882 Planarity : 0.005 0.051 2847 Dihedral : 15.669 167.213 3629 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.77 % Allowed : 21.53 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1992 helix: 1.86 (0.18), residues: 841 sheet: -0.50 (0.29), residues: 303 loop : -0.46 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 435 TYR 0.020 0.002 TYR E 354 PHE 0.045 0.002 PHE E 521 TRP 0.019 0.002 TRP F 101 HIS 0.006 0.001 HIS E 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (17761) covalent geometry : angle 0.69384 / 0.35 (24489) hydrogen bonds : bond 0.04339 / 2.96 ( 823) hydrogen bonds : angle 5.12318 / 3.65 ( 2290) metal coordination : bond 0.00294 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 311 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8564 (tp30) REVERT: A 143 GLN cc_start: 0.9151 (mp10) cc_final: 0.8827 (mp10) REVERT: A 160 GLU cc_start: 0.9038 (pm20) cc_final: 0.8506 (pm20) REVERT: A 211 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7569 (tp30) REVERT: B 28 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8802 (mt-10) REVERT: C 140 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8802 (pp20) REVERT: C 232 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8838 (mt-10) REVERT: D 28 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8886 (mt-10) REVERT: D 113 ASP cc_start: 0.9178 (m-30) cc_final: 0.8856 (m-30) REVERT: E 97 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8819 (tm-30) REVERT: E 98 HIS cc_start: 0.8746 (m90) cc_final: 0.8429 (m90) REVERT: E 104 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8852 (pmm-80) REVERT: E 239 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7972 (mt) REVERT: E 243 PHE cc_start: 0.8309 (m-10) cc_final: 0.8017 (m-10) REVERT: E 250 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7764 (mttt) REVERT: E 280 ASP cc_start: 0.8672 (m-30) cc_final: 0.8072 (p0) REVERT: E 289 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.6968 (ptp-170) REVERT: E 326 PHE cc_start: 0.9101 (m-10) cc_final: 0.8741 (m-80) REVERT: E 361 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7229 (t80) REVERT: E 412 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7028 (mm) REVERT: E 442 ASN cc_start: 0.9389 (t0) cc_final: 0.9093 (t0) REVERT: E 445 GLU cc_start: 0.9298 (tp30) cc_final: 0.9052 (OUTLIER) REVERT: E 449 GLU cc_start: 0.9002 (pt0) cc_final: 0.8527 (pt0) REVERT: E 483 ILE cc_start: 0.9179 (mp) cc_final: 0.8772 (mm) REVERT: E 518 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8163 (tm-30) REVERT: E 523 GLN cc_start: 0.9461 (OUTLIER) cc_final: 0.9168 (mm110) REVERT: E 533 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8459 (p0) REVERT: E 561 GLN cc_start: 0.9603 (mm-40) cc_final: 0.9273 (mm110) REVERT: E 569 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.8974 (tt) REVERT: E 690 GLU cc_start: 0.8607 (mp0) cc_final: 0.8289 (mp0) REVERT: E 771 PHE cc_start: 0.8839 (m-10) cc_final: 0.8526 (m-10) REVERT: E 784 LYS cc_start: 0.9143 (mmpt) cc_final: 0.8815 (tppt) REVERT: F 146 ARG cc_start: 0.9405 (tpp-160) cc_final: 0.8948 (mmp80) REVERT: F 251 ASP cc_start: 0.8915 (m-30) cc_final: 0.8499 (t0) outliers start: 45 outliers final: 20 residues processed: 335 average time/residue: 0.4647 time to fit residues: 176.6430 Evaluate side-chains 315 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 361 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 523 GLN Chi-restraints excluded: chain E residue 533 ASP Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 180 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 13 optimal weight: 0.0070 chunk 164 optimal weight: 8.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.072945 restraints weight = 45612.235| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.31 r_work: 0.2850 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17763 Z= 0.141 Angle : 0.724 12.361 24489 Z= 0.366 Chirality : 0.045 0.480 2882 Planarity : 0.005 0.052 2847 Dihedral : 15.621 173.715 3629 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.77 % Allowed : 22.32 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1992 helix: 1.85 (0.18), residues: 841 sheet: -0.59 (0.29), residues: 310 loop : -0.46 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 782 TYR 0.020 0.001 TYR E 354 PHE 0.040 0.002 PHE E 77 TRP 0.023 0.002 TRP E 433 HIS 0.008 0.001 HIS E 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17761) covalent geometry : angle 0.72406 / 0.37 (24489) hydrogen bonds : bond 0.04196 / 2.87 ( 823) hydrogen bonds : angle 5.05032 / 3.60 ( 2290) metal coordination : bond 0.00183 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8601 (tp30) REVERT: A 143 GLN cc_start: 0.9145 (mp10) cc_final: 0.8819 (mp10) REVERT: A 160 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: A 211 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7569 (tp30) REVERT: B 28 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8789 (mt-10) REVERT: C 79 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9110 (mtpp) REVERT: C 140 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8809 (pp20) REVERT: C 232 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8853 (mt-10) REVERT: D 28 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8896 (mt-10) REVERT: D 113 ASP cc_start: 0.9140 (m-30) cc_final: 0.8822 (m-30) REVERT: D 211 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7535 (tp30) REVERT: E 97 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8804 (tm-30) REVERT: E 98 HIS cc_start: 0.8721 (m90) cc_final: 0.8413 (m90) REVERT: E 104 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8855 (pmm-80) REVERT: E 239 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7667 (pp) REVERT: E 243 PHE cc_start: 0.8214 (m-10) cc_final: 0.7918 (m-10) REVERT: E 280 ASP cc_start: 0.8667 (m-30) cc_final: 0.8066 (p0) REVERT: E 289 ARG cc_start: 0.7423 (tpp-160) cc_final: 0.7013 (ptp-170) REVERT: E 326 PHE cc_start: 0.9106 (m-10) cc_final: 0.8774 (m-80) REVERT: E 412 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.6949 (mm) REVERT: E 442 ASN cc_start: 0.9390 (t0) cc_final: 0.8968 (t0) REVERT: E 444 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8962 (pm20) REVERT: E 445 GLU cc_start: 0.9308 (tp30) cc_final: 0.9056 (tp30) REVERT: E 449 GLU cc_start: 0.9004 (pt0) cc_final: 0.8576 (pt0) REVERT: E 483 ILE cc_start: 0.9152 (mp) cc_final: 0.8746 (mm) REVERT: E 523 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.9172 (mm110) REVERT: E 569 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9181 (tt) REVERT: E 771 PHE cc_start: 0.8817 (m-10) cc_final: 0.8472 (m-10) REVERT: E 782 ARG cc_start: 0.9548 (mtm110) cc_final: 0.9341 (ptp-170) REVERT: E 784 LYS cc_start: 0.9152 (mmpt) cc_final: 0.8827 (tppt) REVERT: F 146 ARG cc_start: 0.9401 (tpp-160) cc_final: 0.8942 (mmp80) REVERT: F 251 ASP cc_start: 0.8921 (m-30) cc_final: 0.8505 (t0) outliers start: 45 outliers final: 24 residues processed: 331 average time/residue: 0.4486 time to fit residues: 168.9976 Evaluate side-chains 324 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 523 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 777 GLU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 95 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 117 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073168 restraints weight = 45641.187| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.36 r_work: 0.2862 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17763 Z= 0.137 Angle : 0.730 14.138 24489 Z= 0.370 Chirality : 0.045 0.462 2882 Planarity : 0.005 0.052 2847 Dihedral : 15.570 179.461 3629 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 2.52 % Allowed : 23.06 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1992 helix: 1.87 (0.18), residues: 841 sheet: -0.47 (0.29), residues: 305 loop : -0.50 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 782 TYR 0.025 0.001 TYR E 59 PHE 0.030 0.002 PHE E 154 TRP 0.029 0.003 TRP F 101 HIS 0.006 0.001 HIS E 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (17761) covalent geometry : angle 0.73044 / 0.37 (24489) hydrogen bonds : bond 0.04186 / 2.87 ( 823) hydrogen bonds : angle 5.00806 / 3.57 ( 2290) metal coordination : bond 0.00134 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8630 (tp30) REVERT: A 143 GLN cc_start: 0.9153 (mp10) cc_final: 0.8806 (mp10) REVERT: A 160 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8605 (pm20) REVERT: A 211 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7545 (tp30) REVERT: B 249 GLU cc_start: 0.8694 (tp30) cc_final: 0.8459 (tp30) REVERT: C 140 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.8815 (pp20) REVERT: C 232 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8860 (mt-10) REVERT: E 97 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8937 (tm-30) REVERT: E 104 ARG cc_start: 0.9287 (pmm-80) cc_final: 0.8829 (pmm-80) REVERT: E 154 PHE cc_start: 0.8924 (p90) cc_final: 0.8267 (m-80) REVERT: E 179 THR cc_start: 0.8580 (p) cc_final: 0.8082 (t) REVERT: E 239 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7640 (pp) REVERT: E 243 PHE cc_start: 0.8144 (m-10) cc_final: 0.7807 (m-10) REVERT: E 280 ASP cc_start: 0.8666 (m-30) cc_final: 0.8053 (p0) REVERT: E 289 ARG cc_start: 0.7504 (tpp-160) cc_final: 0.7156 (ptp-170) REVERT: E 316 PHE cc_start: 0.9116 (m-80) cc_final: 0.8891 (m-10) REVERT: E 326 PHE cc_start: 0.9091 (m-10) cc_final: 0.8780 (m-80) REVERT: E 361 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7311 (t80) REVERT: E 400 LEU cc_start: 0.9137 (mm) cc_final: 0.8901 (mm) REVERT: E 412 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.6616 (mm) REVERT: E 442 ASN cc_start: 0.9377 (t0) cc_final: 0.8966 (t0) REVERT: E 444 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8966 (pm20) REVERT: E 445 GLU cc_start: 0.9330 (tp30) cc_final: 0.8949 (tp30) REVERT: E 449 GLU cc_start: 0.9016 (pt0) cc_final: 0.8563 (pt0) REVERT: E 483 ILE cc_start: 0.9171 (mp) cc_final: 0.8768 (mm) REVERT: E 552 HIS cc_start: 0.8959 (p-80) cc_final: 0.8684 (p90) REVERT: E 569 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9215 (tp) REVERT: E 649 PHE cc_start: 0.8735 (m-80) cc_final: 0.8176 (m-80) REVERT: E 690 GLU cc_start: 0.8552 (mp0) cc_final: 0.8225 (mp0) REVERT: E 771 PHE cc_start: 0.8833 (m-10) cc_final: 0.8500 (m-10) REVERT: E 784 LYS cc_start: 0.9150 (mmpt) cc_final: 0.8827 (tppt) REVERT: F 146 ARG cc_start: 0.9396 (tpp-160) cc_final: 0.8941 (mmp80) REVERT: F 251 ASP cc_start: 0.8892 (m-30) cc_final: 0.8480 (t0) outliers start: 41 outliers final: 23 residues processed: 331 average time/residue: 0.4939 time to fit residues: 185.9695 Evaluate side-chains 314 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 361 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 777 GLU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 0.0170 chunk 156 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 GLN E 590 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.072650 restraints weight = 45320.894| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.31 r_work: 0.2851 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17763 Z= 0.162 Angle : 0.759 15.187 24489 Z= 0.386 Chirality : 0.046 0.450 2882 Planarity : 0.005 0.052 2847 Dihedral : 15.527 175.617 3629 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 2.28 % Allowed : 23.86 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1992 helix: 1.80 (0.18), residues: 842 sheet: -0.44 (0.29), residues: 310 loop : -0.50 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 782 TYR 0.020 0.002 TYR E 59 PHE 0.045 0.002 PHE E 521 TRP 0.040 0.003 TRP E 115 HIS 0.007 0.001 HIS E 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17761) covalent geometry : angle 0.75930 / 0.39 (24489) hydrogen bonds : bond 0.04290 / 2.94 ( 823) hydrogen bonds : angle 5.06017 / 3.62 ( 2290) metal coordination : bond 0.00147 / 0.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8645 (tp30) REVERT: A 143 GLN cc_start: 0.9161 (mp10) cc_final: 0.8798 (mp10) REVERT: A 160 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: A 211 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7568 (tp30) REVERT: B 249 GLU cc_start: 0.8687 (tp30) cc_final: 0.8454 (tp30) REVERT: C 140 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8802 (pp20) REVERT: C 232 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8865 (mt-10) REVERT: E 104 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8892 (pmm-80) REVERT: E 154 PHE cc_start: 0.8944 (p90) cc_final: 0.8247 (m-10) REVERT: E 179 THR cc_start: 0.8593 (p) cc_final: 0.8097 (t) REVERT: E 239 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8195 (mt) REVERT: E 243 PHE cc_start: 0.8164 (m-10) cc_final: 0.7927 (m-10) REVERT: E 280 ASP cc_start: 0.8666 (m-30) cc_final: 0.8042 (p0) REVERT: E 316 PHE cc_start: 0.9133 (m-80) cc_final: 0.8911 (m-10) REVERT: E 326 PHE cc_start: 0.9091 (m-10) cc_final: 0.8777 (m-80) REVERT: E 361 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7324 (t80) REVERT: E 400 LEU cc_start: 0.9197 (mm) cc_final: 0.8992 (mm) REVERT: E 412 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.6883 (mm) REVERT: E 442 ASN cc_start: 0.9396 (t0) cc_final: 0.9104 (t0) REVERT: E 445 GLU cc_start: 0.9337 (tp30) cc_final: 0.8986 (tp30) REVERT: E 449 GLU cc_start: 0.9030 (pt0) cc_final: 0.8577 (pt0) REVERT: E 483 ILE cc_start: 0.9146 (mp) cc_final: 0.8746 (mm) REVERT: E 523 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9184 (mm110) REVERT: E 552 HIS cc_start: 0.8991 (p-80) cc_final: 0.8510 (p-80) REVERT: E 561 GLN cc_start: 0.9553 (mm-40) cc_final: 0.9317 (tp-100) REVERT: E 649 PHE cc_start: 0.8792 (m-80) cc_final: 0.8223 (m-80) REVERT: E 690 GLU cc_start: 0.8626 (mp0) cc_final: 0.8310 (mp0) REVERT: E 771 PHE cc_start: 0.8857 (m-10) cc_final: 0.8422 (m-10) REVERT: E 784 LYS cc_start: 0.9163 (mmpt) cc_final: 0.8841 (tppt) REVERT: F 146 ARG cc_start: 0.9403 (tpp-160) cc_final: 0.8948 (mmp80) REVERT: F 251 ASP cc_start: 0.8900 (m-30) cc_final: 0.8484 (t0) outliers start: 37 outliers final: 23 residues processed: 325 average time/residue: 0.4636 time to fit residues: 171.4051 Evaluate side-chains 317 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 287 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 361 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 523 GLN Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 682 LEU Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 777 GLU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 0.0040 chunk 16 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.072177 restraints weight = 45812.813| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.33 r_work: 0.2848 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.236 17763 Z= 0.260 Angle : 0.888 59.200 24489 Z= 0.490 Chirality : 0.048 0.651 2882 Planarity : 0.005 0.071 2847 Dihedral : 15.526 175.596 3629 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 2.46 % Allowed : 23.92 % Favored : 73.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1992 helix: 1.79 (0.18), residues: 841 sheet: -0.44 (0.29), residues: 310 loop : -0.51 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 782 TYR 0.019 0.001 TYR E 59 PHE 0.034 0.002 PHE E 521 TRP 0.033 0.003 TRP E 115 HIS 0.009 0.001 HIS E 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (17761) covalent geometry : angle 0.88786 / 0.49 (24489) hydrogen bonds : bond 0.04370 / 2.98 ( 823) hydrogen bonds : angle 5.07681 / 3.63 ( 2290) metal coordination : bond 0.00143 / 0.07 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5646.07 seconds wall clock time: 97 minutes 3.69 seconds (5823.69 seconds total)